The present invention pertains to a metal resin composite structure integrating different materials and a manufacturing method thereof, and provides a metal resin composite structure integrating different materials, in which a joining state may be strongly kept by insert-molding a resin composition in a mold after inserting a structure of a metal alloy having fine groove portions and protrusions into the mold. The integral composite structure and the manufacturing method thereof according to the present invention provides the simplification of manufacturing process, low management standards, generalized low-cost chemicals, and further improved tension, thereby improving reliability. In addition, it is possible to realize resin material use at low costs while improving the limitation problems of the resin material use, generated when using the joining technologies according to the conventional art nano methods, thereby increasing applicability in industrial fields.